I've noticed a lot of anime switch between serious and funny these days, Gintama is a special case though because it's actually a comedy anime that tends to go serious every now and then, when it's usually the other way 'round with basically every other series (meaning other series are usually quite serious but tend to have comedic moments, unlike Gintama which is a comedy that has serious moments). I can't think of a comedy that switches to serious like Gintama does.
Isn't D.Gray-Man like 103 episodes long? I've been watching a lot of long anime lately so it might be another one to add to the list. Still plowing through Hajime no Ippo though, up to episode 40. Then comes Eureka Seven.
You watched the Itou Arc yet!?